Genotypes and Genomic Regions Associated With Rhizoctonia solani Resistance in Common Bean

Abstract

Rhizoctonia solani Kühn (teleomorph Thanatephorus cucumeris ) is an important root rot pathogen of common bean ( Phaseolus vulgaris L.). To uncover genetic factors associated with resistance to the pathogen, the Andean (ADP; n = 273) and Middle American (MDP; n = 279) diversity panels, which represent much of the genetic diversity known in cultivated common bean, were screened in the greenhouse using R. solani anastomosis group 2-2. Repeatability of the assay was confirmed by the response of five control genotypes. The phenotypic data for both panels were normally distributed. The resistance responses of ∼10% of the ADP ( n = 28) and ∼6% of the MDP ( n = 18) genotypes were similar or higher than that of the resistant control line VAX 3. A genome-wide association study (GWAS) was performed using ∼200k single nucleotide polymorphisms to discover genomic regions associated with resistance in each panel, For GWAS, the raw phenotypic score, and polynomial and binary transformation of the scores, were individually used as the input data. A major QTL peak was observed on Pv02 in the ADP, while a major QTL was observed on Pv01 with the MDP. These regions were associated with clusters of TIR-NB_ARC-LRR (TNL) gene models encoding proteins similar to known disease resistance genes. Other QTL, unique to each panel, were mapped within or adjacent to a gene model or cluster of related genes associated with disease resistance. This is a first case study that provides evidence for major as well as minor genes involved in resistance to R. solani in common bean. This information will be useful to integrate more durable root rot resistance in common bean breeding programs and to study the genetic mechanisms associated with root diseases in this important societal legume.

Sources of Resistance to Fusarium solani and Associated Genomic Regions in Common Bean Diversity Panels

“…Additionally, VAX3 and Montcalm were resistant and susceptible to Rhizoctonia root rot, respectively, making them excellent choices for control lines to be included in field studies where both Fusarium spp. and Rhizoctonia solani Kühn (teleomorph Thanatephorus cucumeris) are likely playing a role in the root rot complex (Oladzad et al, 2019b). In addition to resistant and susceptible controls, the inclusion of a line consistently displaying a moderate reaction to a quantitative trait like root rot resistance is important to fully characterize lines evaluated in all studies.…”

“…Fusarium root rot severity from the control lines was utilized to evaluate assay reproducibility (Oladzad et al, 2019b). Mean, standard error (SE) of the mean, and coefficients of variability (SE of the mean/mean) were calculated from root rot scores.…”

“…A oneway ANOVA (α = 0.05) was conducted across the four MDP and ADP sub-group evaluations for each control line (Wong and Wilcox, 2000). Estimated relative treatment effects (ranging from 0 to 1), confidence intervals, and P-values were used to determine statistical differences across control lines within each sub-group evaluation (Shah and Madden, 2004;Oladzad et al, 2019b). Significant differences from control lines VAX3, Talon, and Montcalm in MDP and ADP genotypes were based on P-values generated from relative effects and associated 95% confidence intervals were calculated using the LD_CI macro in SAS (Domhof and Langer, 2002;Shah and Madden, 2004).…”

“…In North America and the United States, the most frequently cultivated common beans are members of market classes within races Durango and Mesoamerican of the Middle American genepool and Nueva Granada of the Andean genepool (USDBC 2017). The Andean Diversity Panel (ADP; Cichy et al, 2015) and Middle American Diversity Panel (MDP; Moghaddam et al, 2016) reflect modern genetic diversity in two common bean gene pools and were used extensively to study the genetics of abiotic and biotic stresses in common bean (Zuiderveen et al, 2016;Soltani et al, 2017Soltani et al, , 2018Oladzad et al, 2019b). In 2013, 310 ADP genotypes were evaluated in the field in Minnesota for resistance to root rot (Vasquez-Guzman, 2016).…”

“…Improving the phenotypic methods of screening for resistance provides more robust and accurate phenotypic data that increases the power of GWAS to identify and map resistance QTL. GWAS results can vary based on methods either quantitative or qualitative, used to classify phenotypic data (Oladzad et al, 2019b). Therefore, another important aspect of this study was to develop GWAS results from quantitative, three-class, and binary scoring systems.…”